There are several bosses which has given me challenge due bad chars or wrong chars.
FF7 : All bosses. Weapons and even Sephiroth (last one) in the end of the game. Maybe since all my characters were still 40-55 lvls.. I tried pathetically to lvl them in last place but I died to normal enemies there x]
FF8 : I completed whole game like 5 times, and I never had so much trouble with any boss. If it went tough, I casted aura on Squall and let Lionheart sing.
FF9 : Last boss. Lol, I didnīt bother to exp my characters in this game either, so went to last boss with like 50~ lvl characters.
FF10 & FFX-2 : Maybe this thing, underwater monster in Monster Arena, since I dislike Wakka and Rikku so didnīt bother to lvl them. Nemesis was hard too. Also Dark Aeons a.a
I think so far the hardest bosses were in FF10 for me. Hard to decide which one ^^